| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.6 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.4 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.3 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.2 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.1 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.0 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.2 |
| toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.1 |
| trimmomatic |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| trimmomatic | 0.39 | package |
| coreutils | 8.25 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
readtype|fastq_in: Illumina_SG_R1.fastq readtype|single_or_paired: se operations_0|operation|name: SLIDINGWINDOW output_logs: True output_err: True |
name: value name: value name: value |
Illumina_SG_R1.fastq value |
| Test-2 |
readtype|fastq_in: Illumina_SG_R1.fastq.gz readtype|single_or_paired: se operations_0|operation|name: SLIDINGWINDOW |
name: value |
Illumina_SG_R1.fastq.gz value |
| Test-3 |
readtype|fastq_r1_in: Illumina_SG_R1.fastq.gz readtype|fastq_r2_in: Illumina_SG_R2.fastq.gz readtype|single_or_paired: pair_of_files operations_0|operation|name: SLIDINGWINDOW |
name: value name: value name: value name: value |
Illumina_SG_R1.fastq.gz Illumina_SG_R2.fastq.gz value |
| Test-4 |
readtype|fastq_r1_in: Illumina_SG_R1.fastq readtype|fastq_r2_in: Illumina_SG_R2.fastq readtype|single_or_paired: pair_of_files operations_0|operation|name: SLIDINGWINDOW |
name: value name: value name: value name: value |
Illumina_SG_R1.fastq Illumina_SG_R2.fastq value |
| Test-5 |
readtype|fastq_r1_in: Illumina_SG_R1.fastqillumina readtype|fastq_r2_in: Illumina_SG_R2.fastqillumina readtype|single_or_paired: pair_of_files operations_0|operation|name: SLIDINGWINDOW |
name: value name: value name: value name: value |
Illumina_SG_R1.fastqillumina Illumina_SG_R2.fastqillumina value |
| Test-6 |
readtype|fastq_r1_in: Illumina_SG_R1.fastqsolexa readtype|fastq_r2_in: Illumina_SG_R2.fastqsolexa readtype|single_or_paired: pair_of_files operations_0|operation|name: SLIDINGWINDOW |
name: value name: value name: value name: value |
Illumina_SG_R1.fastqsolexa Illumina_SG_R2.fastqsolexa value |
| Test-7 |
readtype|fastq_in: Illumina_SG_R1.fastq readtype|single_or_paired: se operations_0|operation|crop: 10 operations_0|operation|name: CROP |
name: value |
Illumina_SG_R1.fastq value |
| Test-8 |
readtype|fastq_pair: paired collection readtype|single_or_paired: collection operations_0|operation|name: SLIDINGWINDOW |
Illumina_SG_R1.fastq Illumina_SG_R2.fastq |
|
| Test-9 |
readtype|fastq_pair: paired collection readtype|single_or_paired: collection operations_0|operation|name: SLIDINGWINDOW |
Illumina_SG_R1.fastq.gz Illumina_SG_R2.fastq.gz |
|
| Test-10 |
readtype|fastq_in: Illumina_SG_R1.fastq readtype|single_or_paired: se operations_0|operation|avgqual: 30 operations_0|operation|name: AVGQUAL |
name: value |
Illumina_SG_R1.fastq value |
| Test-11 |
readtype|fastq_in: Illumina_SG_R1.fastq readtype|single_or_paired: se operations_0|operation|target_length: 75 operations_0|operation|strictness: 0.8 operations_0|operation|name: MAXINFO |
name: value |
Illumina_SG_R1.fastq value |
| Test-12 |
readtype|fastq_r1_in: Illumina_SG_R1.fastq readtype|fastq_r2_in: Illumina_SG_R2.fastq readtype|single_or_paired: pair_of_files illuminaclip|adapter_type|adapter_fasta: TruSeq2-PE.fa illuminaclip|do_illuminaclip: True operations_0|operation|name: SLIDINGWINDOW |
name: value name: value name: value name: value |
Illumina_SG_R1.fastq Illumina_SG_R2.fastq value |
| Test-13 |
readtype|fastq_r1_in: Illumina_SG_R1.fastq readtype|fastq_r2_in: Illumina_SG_R2.fastq readtype|single_or_paired: pair_of_files illuminaclip|adapter_type|adapter_text: >PrefixPE/1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >PrefixPE/2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT >PCR_Primer1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >PCR_Primer1_rc AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT >PCR_Primer2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT >PCR_Primer2_rc AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG >FlowCell1 TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC >FlowCell2 TTTTTTTTTTCAAGCAGAAGACGGCATACGA illuminaclip|adapter_type|standard_or_custom: custom illuminaclip|do_illuminaclip: True operations_0|operation|name: SLIDINGWINDOW |
name: value name: value name: value name: value |
Illumina_SG_R1.fastq Illumina_SG_R2.fastq value |
| Test-14 |
readtype|fastq_in: Illumina_SG_R1.fastq readtype|single_or_paired: se operations_0|operation|name: SLIDINGWINDOW quality_score: -phred33 output_logs: True output_err: True |
name: value name: value name: value |
Illumina_SG_R1.fastq value |